bio-gem 0.0.2

data/.document

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+lib/**/*.rb
+bin/*
+- 
+features/**/*.feature
+LICENSE.txt

data/Gemfile

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+source "http://rubygems.org"
+# Add dependencies required to use your gem here.
+# Example:
+#   gem "activesupport", ">= 2.3.5"
+
+# Add dependencies to develop your gem here.
+# Include everything needed to run rake, tests, features, etc.
+group :development do
+  gem "shoulda", ">= 0"
+  gem "bundler", "~> 1.0.0"
+  gem "jeweler", "~> 1.5.1"
+  gem "rcov", ">= 0"
+end

data/Gemfile.lock

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+GEM
+  remote: http://rubygems.org/
+  specs:
+    git (1.2.5)
+    jeweler (1.5.1)
+      bundler (~> 1.0.0)
+      git (>= 1.2.5)
+      rake
+    rake (0.8.7)
+    rcov (0.9.9)
+    shoulda (2.11.3)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  bundler (~> 1.0.0)
+  jeweler (~> 1.5.1)
+  rcov
+  shoulda

data/LICENSE.txt

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+Copyright (c) 2010 Raoul J.P. Bonnal
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.rdoc

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+= bioruby-gem
+
+BioGem is a scaffold generator for those Bioinformaticans who want to start coding an application or a library
+for using/extending BioRuby's core library and sharing it through http://rubygems.org .
+
+The basic idea is to simplify and promote a modular approach to the BioRuby package.
+
+BioGem is not reinventing the wheel just putting together different tools like Jeweler and Bundler modifing their original behaviour when needed. Jeweler is used to create the initial scaffold, setting up git for versioning, releasing it to github.com and/or rubygems.org and packaging. Bundler is used used for setting up a predefined developing environment.
+
+Remind that
+* Jeweler is based on rake
+  $ rake -T
+  in your project directory gives you an overview of the available actions
+
+* GitHub.com and RubyGems.org
+  are two different services and you need to create different accounts for them
+  if you already use GitHub.com you are already all set for using BioGem
+
+== Contributing to bioruby-gem
+ 
+* Check out the latest master to make sure the feature hasn't been implemented or the bug hasn't been fixed yet
+* Check out the issue tracker to make sure someone already hasn't requested it and/or contributed it
+* Fork the project
+* Start a feature/bugfix branch
+* Commit and push until you are happy with your contribution
+* Make sure to add tests for it. This is important so I don't break it in a future version unintentionally.
+* Please try not to mess with the Rakefile, version, or history. If you want to have your own version, or is otherwise necessary, that is fine, but please isolate to its own commit so I can cherry-pick around it.
+
+== Step by Step
+
+* gem install jeweler
+* jeweler bioruby-mystuff
+* cd bioruby_mysuff
+* bundle install
+* rake version:write
+* rake gemspec
+* rake install
+
+Some of these steps have been condensed:
+
+* gem install bio-gem (not yet published on rubygems, grab it from github http://github.com/helios/bioruby-gem and build the gem (gem build bioruby-gem.gemspec; gem install bioruby-gem.gem))
+* $ biogem mystuff
+  * pass just the simple name, it will add bioruby- for the first level directory and for the github repository
+    BUT you'll require the library with bio-mystuff (and this will be the name used on rubygems)
+  * creates a basic gem structure with a default dependencies for bioruby (bio) version 1.4.1
+	    |-- Gemfile
+	    |-- Gemfile.lock
+	    |-- LICENSE.txt
+	    |-- README.rdoc
+	    |-- Rakefile
+	    |-- lib
+	    |   `-- bio-mystuff.rb
+	    |-- data
+	    |   `-- empty but put here your datasets or database(SQLite3?)	
+	    `-- test
+	        |-- helper.rb
+	        `-- test_bio-mystuff.rb
+
+  * $ cd bioruby-mystuff
+  * $ rake version:write (Initial Updated version: 0.0.0)
+  * $ rake gemspec
+* $ rake install (for local test)
+* hack, git add and commit
+* $ rake git:release (remember to create the project first)
+* WHEN you have finished with the hacking you can release the gem by typing:
+  * $ rake release
+
+== NoTes For Developers
+* Update your rubygems environment
+* Keep in mind that Jeweler handles everything is under the control of you git repository, so there is no need to modify the Rakefile or the tasks for including some file, directory etc to you project; just git add your_file_or_directory. Remeber to modify .gitignore to exclude files.
+* Explore the rake tasks with
+  * $ rake -T
+
+== TODO
+* better command line, wrap or reimplement some of the funcionalities provided by Bundler and Jeweler
+
+== Copyright
+
+Copyright (c) 2010 Raoul J.P. Bonnal. See LICENSE.txt for
+further details.
+

data/Rakefile

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+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'rake'
+
+require 'jeweler'
+Jeweler::Tasks.new do |gem|
+  # gem is a Gem::Specification... see http://docs.rubygems.org/read/chapter/20 for more options
+  gem.name = "bio-gem"
+  gem.homepage = "http://github.com/helios/bioruby-gem"
+  gem.license = "MIT"
+  gem.summary = %Q{BioGem helps Bioinformaticians start developing plugins/modules for BioRuby creating a scaffold and a gem package}
+  gem.description = %Q{BioGem is a scaffold generator for those Bioinformaticans who want to start coding an application or a library for using/extending BioRuby core library and sharing it through rubygems.org .
+  The basic idea is to simplify and promote a modular approach to the BioRuby package.}
+  gem.email = "ilpuccio.febo@gmail.com"
+  gem.authors = ["Raoul J.P. Bonnal"]
+  # Include your dependencies below. Runtime dependencies are required when using your gem,
+  # and development dependencies are only needed for development (ie running rake tasks, tests, etc)
+  #  gem.add_runtime_dependency 'jabber4r', '> 0.1'
+  #  gem.add_development_dependency 'rspec', '> 1.2.3'
+  #gem.version='0.0.1'
+end
+Jeweler::RubygemsDotOrgTasks.new
+
+require 'rake/testtask'
+Rake::TestTask.new(:test) do |test|
+  test.libs << 'lib' << 'test'
+  test.pattern = 'test/**/test_*.rb'
+  test.verbose = true
+end
+
+require 'rcov/rcovtask'
+Rcov::RcovTask.new do |test|
+  test.libs << 'test'
+  test.pattern = 'test/**/test_*.rb'
+  test.verbose = true
+end
+
+task :default => :test
+
+require 'rake/rdoctask'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "bio-gem #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

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+0.0.2

data/bin/biogem

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+#!/usr/bin/env ruby
+$LOAD_PATH.unshift File.join(File.dirname(__FILE__), '..', 'lib')
+require 'jeweler/generator'
+require 'bundler'
+require 'bundler/cli'
+require 'fileutils'
+require 'bio-gem'
+require 'rake'
+
+
+orig_argv = ARGV.clone
+if (Jeweler::Generator::Application.run!(*ARGV)==0)
+  pwd = FileUtils.pwd
+  FileUtils.cd "bioruby-#{ARGV.shift}"
+  ARGV << "install"
+  Bundler::CLI.start
+  sh "rake version:write"
+  sh "rake gemspec"
+end

data/bio-gem.gemspec

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+# Generated by jeweler
+# DO NOT EDIT THIS FILE DIRECTLY
+# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
+# -*- encoding: utf-8 -*-
+
+Gem::Specification.new do |s|
+  s.name = %q{bio-gem}
+  s.version = "0.0.2"
+
+  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
+  s.authors = ["Raoul J.P. Bonnal"]
+  s.date = %q{2010-12-21}
+  s.default_executable = %q{biogem}
+  s.description = %q{BioGem is a scaffold generator for those Bioinformaticans who want to start coding an application or a library for using/extending BioRuby core library and sharing it through rubygems.org .
+  The basic idea is to simplify and promote a modular approach to the BioRuby package.}
+  s.email = %q{ilpuccio.febo@gmail.com}
+  s.executables = ["biogem"]
+  s.extra_rdoc_files = [
+    "LICENSE.txt",
+    "README.rdoc"
+  ]
+  s.files = [
+    ".document",
+    "Gemfile",
+    "Gemfile.lock",
+    "LICENSE.txt",
+    "README.rdoc",
+    "Rakefile",
+    "VERSION",
+    "bin/biogem",
+    "bio-gem.gemspec",
+    "lib/bio-gem.rb",
+    "test/helper.rb",
+    "test/test_bio-gem.rb"
+  ]
+  s.homepage = %q{http://github.com/helios/bioruby-gem}
+  s.licenses = ["MIT"]
+  s.require_paths = ["lib"]
+  s.rubygems_version = %q{1.3.7}
+  s.summary = %q{BioGem helps Bioinformaticians start developing plugins/modules for BioRuby creating a scaffold and a gem package}
+  s.test_files = [
+    "test/helper.rb",
+    "test/test_bio-gem.rb"
+  ]
+
+  if s.respond_to? :specification_version then
+    current_version = Gem::Specification::CURRENT_SPECIFICATION_VERSION
+    s.specification_version = 3
+
+    if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
+      s.add_development_dependency(%q<shoulda>, [">= 0"])
+      s.add_development_dependency(%q<bundler>, ["~> 1.0.0"])
+      s.add_development_dependency(%q<jeweler>, ["~> 1.5.1"])
+      s.add_development_dependency(%q<rcov>, [">= 0"])
+    else
+      s.add_dependency(%q<shoulda>, [">= 0"])
+      s.add_dependency(%q<bundler>, ["~> 1.0.0"])
+      s.add_dependency(%q<jeweler>, ["~> 1.5.1"])
+      s.add_dependency(%q<rcov>, [">= 0"])
+    end
+  else
+    s.add_dependency(%q<shoulda>, [">= 0"])
+    s.add_dependency(%q<bundler>, ["~> 1.0.0"])
+    s.add_dependency(%q<jeweler>, ["~> 1.5.1"])
+    s.add_dependency(%q<rcov>, [">= 0"])
+  end
+end
+

data/lib/bio-gem.rb

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+#Overwrite Jeweler classes for properly configure a BioRuby Development Environment/Layout.
+
+class Jeweler
+  class Generator 
+    module  GithubMixin
+      #class Jeweler::Generator::GithubMixin
+      def homepage
+        @homepage ||= "http://github.com/#{github_username}/#{github_repo_name}"
+      end
+      
+      #class Jeweler::Generator::GithubMixin      
+      def git_remote
+        @git_remote ||= "git@github.com:#{github_username}/#{github_repo_name}.git"
+      end
+    end
+    
+      alias original_initialize initialize
+      def initialize(options = {})
+        original_initialize(options)
+        development_dependencies  << ["bio", ">= 1.4.1"]
+      end
+          
+      alias original_project_name project_name  
+      def project_name
+        "bio-#{original_project_name}"
+      end
+      def lib_filename
+         "#{project_name}.rb"
+      end
+      
+      def target_dir
+        project_name.gsub('bio','bioruby')
+      end      
+      alias github_repo_name target_dir
+      
+      def require_name
+        project_name
+      end
+      
+      def data_dir
+        'data'
+      end
+      
+      alias original_create_files create_files
+      # this is the defaul directory for storing library datasets
+      # creates a data directory for every needs.
+      def create_files
+        original_create_files
+        mkdir_in_target data_dir
+      end
+            
+      def create_and_push_repo
+        Net::HTTP.post_form URI.parse('http://github.com/api/v2/yaml/repos/create'),
+                                  'login' => github_username,
+                                  'token' => github_token,
+                                  'description' => summary,
+                                  'name' => github_repo_name
+        # TODO do a HEAD request to see when it's ready?
+        @repo.push('origin')
+      end
+      
+      
+  end
+end
+

data/test/helper.rb

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+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'test/unit'
+require 'shoulda'
+
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+require 'bioruby-gem'
+
+class Test::Unit::TestCase
+end

data/test/test_bio-gem.rb

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+require 'helper'
+
+class TestBiorubyGem < Test::Unit::TestCase
+  should "probably rename this file and start testing for real" do
+    flunk "hey buddy, you should probably rename this file and start testing for real"
+  end
+end

metadata

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+--- !ruby/object:Gem::Specification 
+name: bio-gem
+version: !ruby/object:Gem::Version 
+  prerelease: false
+  segments: 
+  - 0
+  - 0
+  - 2
+  version: 0.0.2
+platform: ruby
+authors: 
+- Raoul J.P. Bonnal
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2010-12-21 00:00:00 +01:00
+default_executable: biogem
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  name: shoulda
+  requirement: &id001 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        segments: 
+        - 0
+        version: "0"
+  type: :development
+  prerelease: false
+  version_requirements: *id001
+- !ruby/object:Gem::Dependency 
+  name: bundler
+  requirement: &id002 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        segments: 
+        - 1
+        - 0
+        - 0
+        version: 1.0.0
+  type: :development
+  prerelease: false
+  version_requirements: *id002
+- !ruby/object:Gem::Dependency 
+  name: jeweler
+  requirement: &id003 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        segments: 
+        - 1
+        - 5
+        - 1
+        version: 1.5.1
+  type: :development
+  prerelease: false
+  version_requirements: *id003
+- !ruby/object:Gem::Dependency 
+  name: rcov
+  requirement: &id004 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        segments: 
+        - 0
+        version: "0"
+  type: :development
+  prerelease: false
+  version_requirements: *id004
+description: |-
+  BioGem is a scaffold generator for those Bioinformaticans who want to start coding an application or a library for using/extending BioRuby core library and sharing it through rubygems.org .
+    The basic idea is to simplify and promote a modular approach to the BioRuby package.
+email: ilpuccio.febo@gmail.com
+executables: 
+- biogem
+extensions: []
+
+extra_rdoc_files: 
+- LICENSE.txt
+- README.rdoc
+files: 
+- .document
+- Gemfile
+- Gemfile.lock
+- LICENSE.txt
+- README.rdoc
+- Rakefile
+- VERSION
+- bin/biogem
+- bio-gem.gemspec
+- lib/bio-gem.rb
+- test/helper.rb
+- test/test_bio-gem.rb
+has_rdoc: true
+homepage: http://github.com/helios/bioruby-gem
+licenses: 
+- MIT
+post_install_message: 
+rdoc_options: []
+
+require_paths: 
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      hash: -2301648142335089709
+      segments: 
+      - 0
+      version: "0"
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      segments: 
+      - 0
+      version: "0"
+requirements: []
+
+rubyforge_project: 
+rubygems_version: 1.3.7
+signing_key: 
+specification_version: 3
+summary: BioGem helps Bioinformaticians start developing plugins/modules for BioRuby creating a scaffold and a gem package
+test_files: 
+- test/helper.rb
+- test/test_bio-gem.rb